From noreply at r-forge.r-project.org Mon Nov 23 10:54:36 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 23 Nov 2015 10:54:36 +0100 (CET) Subject: [Patchwork-commits] r219 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/TAPS/R Message-ID: <20151123095437.0452818482E@r-forge.r-project.org> Author: sebastian_d Date: 2015-11-23 10:54:36 +0100 (Mon, 23 Nov 2015) New Revision: 219 Modified: .git/index .git/logs/HEAD .git/logs/refs/heads/master .git/logs/refs/remotes/origin/master .git/refs/heads/master .git/refs/remotes/origin/master pkg/TAPS/R/TAPS.r Log: Bjorn and Markus buggfixing Modified: .git/index =================================================================== (Binary files differ) Modified: .git/logs/HEAD =================================================================== --- .git/logs/HEAD 2015-10-19 11:55:17 UTC (rev 218) +++ .git/logs/HEAD 2015-11-23 09:54:36 UTC (rev 219) @@ -101,3 +101,4 @@ b5798bb1874d9dc8e50fa5083961a8836d79f76c 52402622419759bc3642b6f49dd0f4abd2003d38 Sebastian DiLorenzo 1434615906 +0200 pull: Fast-forward 52402622419759bc3642b6f49dd0f4abd2003d38 4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 Sebastian DiLorenzo 1435303966 +0200 pull: Fast-forward 4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 0a1de5c432ad323bbac1093425e9a939f351b50b Sebastian DiLorenzo 1445255649 +0200 pull: Fast-forward +0a1de5c432ad323bbac1093425e9a939f351b50b 0b2b81a68a67ce90b6f3c8d65b3cbab6636348b7 Sebastian DiLorenzo 1448272403 +0100 pull: Fast-forward Modified: .git/logs/refs/heads/master =================================================================== --- .git/logs/refs/heads/master 2015-10-19 11:55:17 UTC (rev 218) +++ .git/logs/refs/heads/master 2015-11-23 09:54:36 UTC (rev 219) @@ -101,3 +101,4 @@ b5798bb1874d9dc8e50fa5083961a8836d79f76c 52402622419759bc3642b6f49dd0f4abd2003d38 Sebastian DiLorenzo 1434615906 +0200 pull: Fast-forward 52402622419759bc3642b6f49dd0f4abd2003d38 4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 Sebastian DiLorenzo 1435303966 +0200 pull: Fast-forward 4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 0a1de5c432ad323bbac1093425e9a939f351b50b Sebastian DiLorenzo 1445255649 +0200 pull: Fast-forward +0a1de5c432ad323bbac1093425e9a939f351b50b 0b2b81a68a67ce90b6f3c8d65b3cbab6636348b7 Sebastian DiLorenzo 1448272403 +0100 pull: Fast-forward Modified: .git/logs/refs/remotes/origin/master =================================================================== --- .git/logs/refs/remotes/origin/master 2015-10-19 11:55:17 UTC (rev 218) +++ .git/logs/refs/remotes/origin/master 2015-11-23 09:54:36 UTC (rev 219) @@ -98,3 +98,4 @@ b5798bb1874d9dc8e50fa5083961a8836d79f76c 52402622419759bc3642b6f49dd0f4abd2003d38 Sebastian DiLorenzo 1434615905 +0200 pull: fast-forward 52402622419759bc3642b6f49dd0f4abd2003d38 4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 Sebastian DiLorenzo 1435303966 +0200 pull: fast-forward 4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 0a1de5c432ad323bbac1093425e9a939f351b50b Sebastian DiLorenzo 1445255649 +0200 pull: fast-forward +0a1de5c432ad323bbac1093425e9a939f351b50b 0b2b81a68a67ce90b6f3c8d65b3cbab6636348b7 Sebastian DiLorenzo 1448272403 +0100 pull: fast-forward Modified: .git/refs/heads/master =================================================================== --- .git/refs/heads/master 2015-10-19 11:55:17 UTC (rev 218) +++ .git/refs/heads/master 2015-11-23 09:54:36 UTC (rev 219) @@ -1 +1 @@ -0a1de5c432ad323bbac1093425e9a939f351b50b +0b2b81a68a67ce90b6f3c8d65b3cbab6636348b7 Modified: .git/refs/remotes/origin/master =================================================================== --- .git/refs/remotes/origin/master 2015-10-19 11:55:17 UTC (rev 218) +++ .git/refs/remotes/origin/master 2015-11-23 09:54:36 UTC (rev 219) @@ -1 +1 @@ -0a1de5c432ad323bbac1093425e9a939f351b50b +0b2b81a68a67ce90b6f3c8d65b3cbab6636348b7 Modified: pkg/TAPS/R/TAPS.r =================================================================== --- pkg/TAPS/R/TAPS.r 2015-10-19 11:55:17 UTC (rev 218) +++ pkg/TAPS/R/TAPS.r 2015-11-23 09:54:36 UTC (rev 219) @@ -221,7 +221,6 @@ } # cat('..plotting.\n') - #browser() OverviewPlot(regs$chr,regs$start,regs$end,regs$logs,regs$scores,hg18=hg18, as.character(Log2$Chromosome),Log2$Start,Log2$Value,as.character(alf$Chromosome),alf$Start,alf$Value, name=name,MAPD=sampleData$MAPD[i],MHOF=sampleData$MHOF[i]) @@ -519,8 +518,8 @@ try(xx <- kmeans(t1, 2),silent=T) ## Attempt k-means (Hartigan-Wong: has proven very stable) if (!is.null(xx)) if (min(xx$size) > 0.05*max(xx$size)) { ## On some occations data quality is poor, requiring 5%+ heterozygous SNPs avoids most such cases. xx=xx$centers - } else xx=NA - } else xx=NA + } else xx=median(t1,na.rm = T) + } else xx=median(t1,na.rm = T) } else xx=NA #try (if (is.na(xx)) xx=0:1, silent=T) #try (if (length(xx)==0) xx=0:1, silent=T) @@ -2218,7 +2217,7 @@ #Add axis to the left & right of signal axis(side=2,tck=-0.025,at=seqminmax,cex.axis=0.6,pos=0,las=1) - axis(side=4,tck=-0.025,at=seqminmax,cex.axis=0.6,pos=max(mpos),las=1) + axis(side=4,tck=-0.025,at=seqminmax,cex.axis=0.6,pos=sum(chroms$length),las=1) mtext("Log-ratio",side=2,line=0) #Add grey segments @@ -2249,7 +2248,7 @@ #Add a bar between chromosomes to distinguish them segments( - x0=c(chroms$before,sum(chroms$length),max(mpos)),x1=c(chroms$before,sum(chroms$length),max(mpos)), + x0=c(chroms$before,sum(chroms$length)),x1=c(chroms$before,sum(chroms$length)), y0=-100,y1=100, col='#000000', lwd=1) @@ -2327,13 +2326,13 @@ #Add axis to the left,right and below of AI. The below axis is the chromosome numbers 1-24. axis(side=2,tck=-0.04,at=seq(from=0,to=1,by=0.2),cex.axis=0.6,pos=0,las=1) axis(side=1,at=pre,pos=0,labels=c(seq(from=1,to=22),"X",'Y'),cex.axis=0.55,lty=0)#,tck=0,col.ticks='#00000000') - axis(side=4,tck=-0.04,at=seq(from=0,to=1,by=0.2),cex.axis=0.6,pos=max(mpos),las=1) # + axis(side=4,tck=-0.04,at=seq(from=0,to=1,by=0.2),cex.axis=0.6,pos=sum(chroms$length),las=1) # mtext("Allele frequency",side=2,line=0) mtext("Chromosomes",side=1,line=1.5,adj=0.4) #Add a bar between chromosomes to distinguish them segments( - x0=c(chroms$before,sum(chroms$length),max(mpos)),x1=c(chroms$before,sum(chroms$length),max(mpos)), + x0=c(chroms$before,sum(chroms$length)),x1=c(chroms$before,sum(chroms$length)), y0=0,y1=100, col='#000000', lwd=1) @@ -2403,6 +2402,8 @@ #Select the chromosome this <- chroms[chroms$c==c,] + #Skip current chromosome if it doesn't exist. + if(!any(as.character(this$chr) == chr)) next() if(nrow(this) == 0) next #Initialize jpeg